With the Wisconsin Timber Rattlers in 2009, the youngster was 4-4 with a save, 3.47 ERA and 118 K in 103 2/3 innings. The hard-throwing right-hander (peak of 95 mph) was ranked by Baseball America as the Midwest League's #14 prospect, between A.J. Pollock and James Darnell. He split 2010 between the Brevard County Manatees (6-3, 3.86) and Huntsville Stars (2-3, 3.61) with a drop-off in his K rate (104 in 147 1/3 IP) and more walks (64). Baseball America rated him as the third-best Brewers prospect going into 2011.

In 2011, Peralta improved on his prior season. He was 9-7 with a 3.46 ERA for Huntsville, fanning 117 in 119 2/3 IP, then was 2-0 with a 2.03 ERA and 40 K in 31 IP in 5 games for the AAA Nashville Sounds. He led the Southern League in ERA by .20 over Andrew Carraway but lost All-Star right-handed pitcher honors to Nathan Eovaldi. He was among the Milwaukee farm chain leaders in wins (second to Michael Fiers) and strikeouts (3 shy of leader Tyler Thornburg). Among Milwaukee minor leaguers with 100+ innings, only Fiers and Thornburg had lower ERAs. Baseball America rated him as the #8 prospect in the Southern League, between Randall Delgado and Yasmani Grandal and as the top Milwaukee prospect (56th overall in the majors) entering 2012.

In winter ball in 2011-2012, Peralta was 1-3 with a 4.68 ERA for the Gigantes del Cibao. Peralta began the summer of 2012 back with Nashville and was very sharp in his first three outings (0-1, 2.13, 9 H in 17 IP). He was called up to the major leagues when Chris Narveson got hurt.

In 2014, Wily came out of nowhere to become the first 14-game winner in the major leagues that season on August 7th, when the Brewers defeated the San Francisco Giants, 3-1. Peralta had not even been a mid-season All-Star, but won five consecutive starts beginning on July 13th to catch the major league win leaders and then pass them. He was helped by the fact that Masahiro Tanaka had been sidelined by an arm injury and Mark Buehrle had run into trouble after starting the season racking up the W's. The win improved Wily's record to 14-6, 3.42, in 23 starts. The streak of wins ended when he lost to the Chicago Cubs, 3-1, on August 12th, giving an 0-3 mark against the NL Central doormats that season. After Johnny Cueto beat him to the punch as the majors first 15-game winner, he notched his own win number 15 on August 17th with a 7-2 road win over the Los Angeles Dodgers.